Abstract: A method and system for fabricating semiconductor wafers is disclosed, wherein a rugged and/or smooth, atomically clean, semiconductor substrate is provided in a rapid thermal processing ("RTP") chamber. The substrate can be single crystal, polycrystalline or amorphous silicon. In one embodiment of the present invention, the substrate is cleaned by exposing it to at least one of CF.sub.4, C.sub.2 F.sub.2, C.sub.2 F.sub.6, C.sub.4 F.sub.8, CHF.sub.3, HF, NF.sub.6, and NF.sub.3 diluted with Ar-H.sub.2 at a temperature substantially within the range of 650.degree. C. to 1150.degree. C. for approximately 10 to 60 seconds in the chamber. Subsequently, the clean substrate is exposed to a first gas and energy generating a first temperature substantially within the range of 650.degree. C. to 1150.degree. C. in situ under substantially high vacuum for approximately 5 seconds to 20 seconds. Simultaneous to exposing the substrate to the first gas, a second gas comprising fluorine as an oxidizing agent, preferably NF.